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The Complete Mitochondrial Genome of Two Tetrag- Natha Spiders (Araneae: Tetragnathidae): Severe Trun- Cation of Trnas and Novel

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The Complete Mitochondrial Genome of Two Tetrag- Natha Spiders (Araneae: Tetragnathidae): Severe Trun- Cation of Trnas and Novel Int. J. Biol. Sci. 2016, Vol. 12 109 Ivyspring International Publisher International Journal of Biological Sciences 2016; 12(1): 109-119. doi: 10.7150/ijbs.12358 Research Paper The Complete Mitochondrial Genome of two Tetrag- natha Spiders (Araneae: Tetragnathidae): Severe Trun- cation of tRNAs and Novel Gene Rearrangements in Araneae Zheng-Liang Wang #, Chao Li #, Wen-Yuan Fang and Xiao-Ping Yu Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, People’s Republic of China # These authors contributed equally to this paper. Corresponding author: X.-P. Yu, Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, People’s Republic of China. Phone and fax: 86-571-86836006. E-mail: [email protected]. © Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions. Received: 2015.04.09; Accepted: 2015.10.26; Published: 2016.01.01 Abstract Mitogenomes can provide information for phylogenetic analysis and evolutionary biology. The Araneae is one of the largest orders of Arachnida with great economic importance. In order to develop mitogenome data for this significant group, we determined the complete mitogenomes of two long jawed spiders Tetragnatha maxillosa and T. nitens and performed the comparative analysis with previously published spider mitogenomes. The circular mitogenomes are 14578 bp long with A+T content of 74.5% in T. maxillosa and 14639 bp long with A+T content of 74.3% in T. nitens, respectively. Both the mitogenomes contain a standard set of 37 genes and an A+T-rich region with the same gene orientation as the other spider mitogenomes, with the exception of the dif- ferent gene order by the rearrangement of two tRNAs (trnW and trnG). Most of the tRNAs lose TΨC arm stems and have unpaired amino acid acceptor arms. As interesting features, both trnSAGN and trnSUCN lack the dihydrouracil (DHU) arm and long tandem repeat units are presented in the A+T-rich region of both the spider mitogenomes. The phylogenetic relationships of 23 spider mitogenomes based on the concatenated nucleotides sequences of 13 protein-coding genes in- dicated that the mitogenome sequences could be useful in resolving higher-level relationship of Araneae. The molecular information acquired from the results of this study should be very useful for future researches on mitogenomic evolution and genetic diversities in spiders. Key words: Mitogenome; Araneae; Tetragnatha maxillosa; Tetragnatha nitens; Phylogeny Introduction Generally, the arthropod mitogenome is a circu- nome size, maternal inheritance, high rate of evolu- lar, double-stranded molecule, ranging in size from 14 tion and low level of intermolecular genetic recom- kb to 20 kb, usually containing a standard set of 13 bination, the mitogenome has been widely regarded protein-coding genes (PCGs), two ribosomal RNA as an effective molecular marker for molecular evolu- genes (the large and small ribosomal subunits, tion, phylogenetic studies, population genetics and rRNAs), 22 transfer RNA genes (tRNAs) and an phylogeography [2]. Moreover, the information of A+T-rich region in a highly variable length with es- gene rearrangement, tRNA secondary structure, ge- sential regulatory elements for replication and tran- netic code alteration and models of control of replica- scription [1]. Due to the characteristics of small ge- tion and transcription in the complete mitogenome http://www.ijbs.com Int. J. Biol. Sci. 2016, Vol. 12 110 data are also extensively exploited for deep-level Materials and methods phylogenetic inference at various taxonomic levels in the past decade [3,4]. Sample collection and DNA extraction Spiders (Araneae) are among the largest animal Specimens of spiders, T. maxillosa and T. nitens groups in the world due to their broad diversity, were collected from the paddy fields in Yuyao world-wide distribution and conspicuous synapo- (E121°09′, N30°03′), Zhejiang Province, China. The morphies [5]. Approximately 45,000 described species field collections did not involve endangered or pro- in 114 families make Araneae the seventh-largest or- tected species and no specific permits were required der next to the five largest insect orders (Coleoptera, for our collecting. All collections were preserved in Hymenoptera, Lepidoptera, Diptera and Hemiptera) 95% ethanol and stored in the temperature cabinet at and Acari among the Arachnida [6]. Due to such high 4°C. Total genomic DNA was extracted from leg tis- species diversity, there are many taxonomic problems sue of each spider individual of the two Tetragnatha about the order Araneae which remain to be unsolved species using the DNeasy Tissue Kit (Qiagen, Hilden, [7,8]. Because of homoplasies or reduction of ana- Germany) according to the manufactures protocol. tomical characters in morphological and ethological data [5], it would be desirable to examine an inde- PCR amplification, cloning and sequencing pendent set of molecular data. Partial mitochondrial Primer sequences of long PCR amplification gene sequences of cytochrome oxidase subunit 1 were designed based on the conserved sequences (COI), rRNAs (16S and 12S) and tRNAs, and nuclear which were obtained by aligning the complete mito- genes of rDNA (18S and 28S) and histone (H3) from genome sequences of four spider species that were spiders have been documented and extensively used downloaded from GenBank: Habronattus oregonnesis for phylogenetic analysis [9,10]. However, these short (NC_005942), Heptathela hangzhouensis (NC_005924), mitochondrial or nuclear genes usually lack the phy- Nephila clavata (NC_008063) and Telamonia vlijmi logenetic information in resolving phylogenetic rela- (NC_024287). The six primer sets that were used to tionships among families or subfamilies within one amplify overlapping fragments of the complete mi- order and sometimes resulted in controversial signal togenome of T. maxillosa and T. nitens are shown in [8,11]. Hence, additional reliable data sets for phylo- Table S1. genetic reconstructions, such as the complete mito- All PCRs were performed using TaKaRa LA PCR genome sequences, are required. Amplification Kit Version 2.1 (Takara Co., Dalian, To date, more than 130 complete mitogenomes China) with the following amplification condition: an from species of arachnids have been determined, but initial denaturation for 5 min at 95°C, followed by 40 only 21 species in 14 families from Araneae were cycles of denaturation for 10s at 92°C, annealing for publicly available in GenBank. These 21 mitogenomes 30s at 50°C, elongation for 4 min at 68°C in the initial share a similar molecular size, ranging from 13,874 bp 20 cycles and then increase by 20s per cycle in the final in Ornithoctonus huwena [12] to 14,741 bp in Wadicosa 20 cycles and a final extension step for 10 min at 72°C. fidelis [13], but have variations in mitogenomic char- All PCR products were resolved by electrophoresis in acteristics, such as gene content and gene arrange- 1.0% agarose gel, purified with DNA Gel Purification ment. Arachnid mitogenomes, in particular spider Kit (TianGen, China), ligated to the pGEM-T-Easy mitogenomes, possess compact mitogenomes and vector (Promega,USA) and sequenced using DNA their tRNAs usually lack the sequence for the T-arm Sequencer (ABI377) at Sangon Inc (Shanghai, China). and a paired aminoacyl stem of the cloverleaf struc- ture. Such atypical tRNAs might be modified by Sequencing assembling and annotation post-transcriptional editing to be functional [14]. The complete mitogenome sequences were as- In the present study, we sequenced and anno- sembled using the Staden package 1.7.0 [15]. PCGs tated the complete mitogenome sequences of two long and rRNAs were initially identified via the MITOS jawed spiders Tetragnatha maxillosa and T. nitens web server [16] and subsequently refined by hand (Araneae: Tetragnathidae), which are the dominant annotation method following the procedures pro- arthropod predators in the agroecological system. 21 posed by Cameron [17]. Gene boundaries were de- spider mitogenomes that are available in GenBank termined by comparing with gene regions from pre- were used in the comparative analysis to reveal the viously characterized spider mitogenomes: W. fidelis gene rearrangements in two Tetragnatha species. Ad- [13], O. huwena and H. hangzhouensis [12]. tRNAs were ditionally, phylogenetic study was also performed to identified by tRNAscan-SE 1.2.1 [18] and ARWEN assess the utility of mitogenome data to understand 1.2.3.c [19]. The putative tRNAs which were not found higher phylogeny of Araneae. by the two software tools were identified based on sequence similarity to tRNAs of the other previously http://www.ijbs.com Int. J. Biol. Sci. 2016, Vol. 12 111 published spider mitogenomes. Nucleotide composi- other spider mitogenomes available from GenBank tion and codon usage were calculated in MEGA 4.0 [13]. Both mitogenomes share the same 37 typical [20]. Potential inverted repeats or palindromes in the metazoan gene set (13 PCGs, 22 tRNAs and two A+T-rich region were determined using Tandem Re- rRNAs) and an A+T-rich region [1]. Among these 37 peats Finder (http://tandem.bu.edu/trf/trf.html) genes, twenty-three are coded on the major strand with the default parameters [21]. (J-strand) while the rest are coded on the minor strand AT-skew=(A–T)/(A+T) and GC-skew=(G–C)/(G+C) (N-strand). Gene orientation of T. maxillosa and T. were used to measure the nucleotide compositional nitens mitogenomes is identical to that of all previ- difference between genes [22]. ously determined araneoid mitogenomes [27,28]. The complete mitogenome sequences of T. max- With the exception of eight translocated tRNAs, mi- illosa and T. nitens have been deposited in the Gen- togenome gene order of the two species are similar to Bank database under accession number KP306789 and that of L.
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